RNA-seq and DNA methylomes of germinating rice and developing coleoptiles (RNA-Seq)
Ontology highlight
ABSTRACT: RNAseq profiling of seeds and 7 time points during germination in rice under aerobic and anerobic conditions, as well as following re-oxygenation.
Project description:methylC-seq profiling of seeds, at 0 h and 24 h after imbibition and following 4-d of growth under aerobic and anerobic conditions, as well as following re-oxygenation (3dN1dA) in rice.
Project description:Seed germination is a complicated physiological process, during which structures of mitochondria and plastids are recovered, and metabolisms are re-activated (Han and Yang, 2015). It has been shown that metabolism reactivation is very important for rice germination (He et al., 2011b;Han et al., 2014a). It is still unknown if protein acetylation involved in and regulate these metabolisms during rice seed germination. To answer this question, we globally profiled the acetylome in rice embryos from the germinating seeds. A number of acetylated enzymes were identified. The results provide more information about the metabolism regulation in germinating seeds.
Project description:The dehulled rice (Oryza sativa L. japonica. cv. Nipponbare) seeds were washed with distilled water for three times and then imbibed with distilled water in dark growth chamber at 26 °C and 70% relative humidity. About 100 embryos (50 mg) of rice seeds were sliced manually and collected at intervals of 24h after imbibitions (HAI), respectively. After frozen with liquid nitrogen, the samples were stored in −80 °C until used for protein extraction.
Project description:To establish the basis for understanding molecular mechanism of seed germination response to temperature, we analyzed transcriptomes in freshly harvested dormant and dry stored after-ripened seeds. The after-ripened seeds started to show visible germination from 36h after the start of imbibition, and almost all the seeds germinated after 3 days. The freshly harvested seeds stayed dormant by imbibition at 26°C, and germination of the after-ripened seeds was almost completely inhibited at 34°C. Total RNA was prepared from 0 (dry), 6 and 24h imbibed seeds to find regulatory genes of seed dormancy and germination.
Project description:Rice (Oryza sativa L.) seeds can germinate in complete absence of oxygen. Under anoxia, the rice coleoptile elongates, reaching a length greater than that of the aerobic one. In this series, we compare the transcriptome of rice coleoptiles grown under aerobic and anaerobic conditions. Lasanthi-Kudahettige, R, et. al. Plant Physiology (2007). Transcript Profiling of the Anoxic Rice Coleoptile. Keywords: stress response
Project description:Sucrose non-fermenting-1-related protein kinase 1 (SnRK1) is a central regulator of metabolism and developmental transition in plant. Compound 991 is a well-known 5′-adenosine monophosphate activated protein kinase (AMPK) activator in mammals. SnRK1 and AMPK are highly conserved. However, whether 991 could also act as a SnRK1 activator is unknown. Adding 991 significantly increased the activity of SnRK1 in desalted extracts from germinating rice seeds in vitro. To determine whether 991 has biological activity in plant, rice seeds were treated with different concentrations of 991. Low concentration of 991 promoted rice seed germination, while high concentration of 991 inhibited rice germination. The effect of 991 on rice germination is similar to the effect of OsSnRK1a overexpression on germination. To explore whether 991 affects germination by specifically affecting SnRK1, the germination status of the snrk1a mutant and WT under 1 μM 991 treatment were compared. The snrk1a mutant exhibited insensitivity to 991. Through phosphoproteomic analysis, we found that the differential phosphopeptides caused by 991 treatments and overexpression of OsSnRK1a are largely overlapped. Phosphoproteomic analysis also revealed that SnRK1 might affect rice germination by regulating the phosphorylation levels of S285-PIP2;4, S1013-SOS1 and S110-ABI5. These results showed that 991 is a specific and workable SnRK1 activator in rice. The promotion and inhibition of 991 treatments on germination also exist in wheat seeds. 991 is expected to be used for exploring the function of SnRK1 in more detail and depth and chemical regulation of growth and development in crops.
Project description:affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30°C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in “E” while the endosperm samples are abbreviated “A”. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition).
Project description:affy_rice_2012_01 - ivt - One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.-We applied a Controlled Deterioration Treatment (CDT) to seeds from the reference rice cultivar Nipponbare. First, all seeds are equilibrated at 25°C and 85% relative hygrometry. Then, depending on the treatment, seeds are placed at 25, 40 or 45°C in 85% relative hygrometry before being finally equilibrated at 25°C and 32% relative hygrometry. The germination of the three seed batches was measured during five days with one measure every 8h. Seeds placed at 25°C during the whole experiment were similar to control seeds kept in the fridge and germinated at nearly 100% in 48h. Seeds placed at 40°C during 15 days germinate at 74% but show altered seedling phenotypes (loss of seed vigor). Finally, seeds placed at 45°C do not germinate.
Project description:affy_rice_2012_01 - ovation - One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.-We applied a Controlled Deterioration Treatment (CDT) to seeds from the reference rice cultivar Nipponbare. First, all seeds are equilibrated at 25°C and 85% relative hygrometry. Then, depending on the treatment, seeds are placed at 25, 40 or 45°C in 85% relative hygrometry before being finally equilibrated at 25°C and 32% relative hygrometry. The germination of the three seed batches was measured during five days with one measure every 8h. Seeds placed at 25°C during the whole experiment were similar to control seeds kept in the fridge and germinated at nearly 100% in 48h. Seeds placed at 40°C during 15 days germinate at 74% but show altered seedling phenotypes (loss of seed vigor). Finally, seeds placed at 45°C do not germinate.
Project description:affy_rice_2012_01 - ovation - One of the key questions for future agriculture will be to save agronomical relevant biodiversity. To do so, it is important to select the best crop cultivars that will germinate efficiently (good seed vigor) and for a long period of time (good seed longevity). Surprisingly, while mankind rely heavily on cereals, very few studies have identified genes positively related to cereal seed vigor and longevity. To close this scientific gap, we aimed to identify genes positively involved in rice seed vigor and longevity. We thus used a “controlled deterioration treatment (Tesnier et al., 2002) to mimic natural seed ageing. Seeds are first equilibrated at 25°C and 85% relative hygrometry during three days. Then, during 15 days, three different batch of seeds are either (i) kept at 25°C and 85% RH (control seeds), (ii) placed at 40°C and 85% RH (loss of seed vigor) or (iii) placed at 45°C and 85% RH (loss of germination capacity). Finally, seeds are equilibrated at 25°C and 32% RH during three days. Using this CDT treatment, we obtained rice seeds with contrasted seed vigor or germination capacity. We extracted the total RNA from the embryos and we analysed their transcriptome using the Affymetrix Rice Genome Array.-We applied a Controlled Deterioration Treatment (CDT) to seeds from the reference rice cultivar Nipponbare. First, all seeds are equilibrated at 25°C and 85% relative hygrometry. Then, depending on the treatment, seeds are placed at 25, 40 or 45°C in 85% relative hygrometry before being finally equilibrated at 25°C and 32% relative hygrometry. The germination of the three seed batches was measured during five days with one measure every 8h. Seeds placed at 25°C during the whole experiment were similar to control seeds kept in the fridge and germinated at nearly 100% in 48h. Seeds placed at 40°C during 15 days germinate at 74% but show altered seedling phenotypes (loss of seed vigor). Finally, seeds placed at 45°C do not germinate. 6 arrays - rice; treated vs untreated comparison